DNA Sequence Alignment

Sequence alignment visualization and editing. Annotations. Select from multiple algorithms.

Awesome sequence alignment visualization and editing

  • Show annotations on the alignment and edit at the same time
  • Drag to remove or insert gaps
  • Join sequences together
  • Strip columns
  • Type directly into an alignment
  • Correct bad calls
  • Viewing and coloring by translation alongside allows you to correct coding sequences
  • View phylogeny alongside the alignment and link back to a tree
  • Similarity and sequence logo graphs
  • Real-time updates to the statistics panel (real-time) update according to selection
  • Spot disagreements easily with highlighting

Access a variety of DNA alignments including Clustal Omega, MUSCLE and MAFFT from within one software program

Save time and stop jumping around from program to program. Select a specific task to perform without leaving Geneious. Built in alignments include:

  • The Geneious Aligner
  • Clustal Omega
  • Local Re-alignment
  • Pairwise alignment
  • Translation Align
  • Consensus Align
  • MAFFT- available as a plugin
  • MAUVE- available as a plugin
  • LastZ – available as plugin

Your data your way

No matter what alignment you choose, the data is still yours to edit and annotate in a way that works for you.

Better genome alignments are just a few clicks away.

Introduction to Multiple Alignments

Aligning Bacterial Genomes with Mauve


Pairwise Alignment – Develop the skills needed to align pairs of DNA and protein sequences with Geneious using dotplots and alignment algorithms.

Aligning Bacterial Genomes with Mauve – Learn how to align bacterial genomes using the Mauve plugin for Geneious. This tutorial covers alignment of complete genomes and ordering of draft genomes against a reference.

More Geneious Prime Features

Assembly and MappingDe novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.

NGS Visualization and Analysis – Comprehensive analysis of data, including genome browser, contig visualization, SNP calling, and RNA-Seq expression analysis.

Phylogenetic TreesBuild phylogenetic trees using peer-reviewed algorithms, including RAxML and PAUP*

Molecular Cloning – View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson, and Gateway cloning.

BLAST / NCBI – Connect to NCBI and PubMed, submit sequences directly to GenBank, BLAST sequences and search your own database.

Import Data – Import and convert common file types as well as their annotations and notes with a simple drag and drop

Geneious is paramount in my research so I can’t be without it for too long.
Bob LitermanIowa State University